BACKGROUND: Administrative datasets are often used to assess outcomes and quality of pediatric cardiac programs; however their accuracy regarding case ascertainment is unclear. We linked patient data (2004-2010) from the Society of Thoracic Surgeons Congenital Heart Surgery (STS-CHS) Database (clinical registry) and the Pediatric Health Information Systems (PHIS) database (administrative database) from hospitals participating in both to evaluate differential coding/classification of operations between datasets and subsequent impact on outcomes assessment. METHODS: Eight individual benchmark operations and the Risk Adjustment in Congenital Heart Surgery, version 1 (RACHS-1) categories were evaluated. The primary outcome was in-hospital mortality. RESULTS: The cohort included 59,820 patients from 33 centers. There was a greater than 10% difference in the number of cases identified between data sources for half of the benchmark operations. The negative predictive value (NPV) of the administrative (versus clinical) data was high (98.8%-99.9%); the positive predictive value (PPV) was lower (56.7%-88.0%). Overall agreement between data sources in RACHS-1 category assignment was 68.4%. These differences translated into significant differences in outcomes assessment, ranging from an underestimation of mortality associated with truncus arteriosus repair by 25.7% in the administrative versus clinical data (7.01% versus 9.43%; p = 0.001) to an overestimation of mortality associated with ventricular septal defect (VSD) repair by 31.0% (0.78% versus 0.60%; p = 0.1). For the RACHS-1 categories, these ranged from an underestimation of category 5 mortality by 40.5% to an overestimation of category 2 mortality by 12.1%; these differences were not statistically significant. CONCLUSIONS: This study demonstrates differences in case ascertainment between administrative and clinical registry data for children undergoing cardiac operations, which translated into important differences in outcomes assessment.